Stitch Interactive Report Run: h9C12WT_mc
Generated at 2024-09-19 17:11:50
High decoy scores
The highest scoring decoy template scores at least 50% of the actual templates in template matching. Look into the Decoy segment for more details.
Maybe the origin of this issue is one of the following:
A sample with very high background noise, in that case the result should be thoroughly checked by hand.
Incorrect segments chosen, the chosen segments should match the expected segments and species of the dataset.
Ineffective segment joining
The segment joining between IGHV and IGHJ did not find a good solution, look into the specific report to see if this influences the validity of the results.
Homo sapiens Heavy Chain
QVQLKQSGPGLLQPSQRLSLTCTVSGFSIGRGGGGSGGFIRQSPGKGLEWIGVIWRRGSTCYNPSLKSLVNISLDTSKNQVSLSLSAVQEADLAVYFPQRGQQSGNFPLAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSVSTVVTVPSSSLTTQTYIRNVNHKPSNTKVCKKVQQKSYDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTPNRQEQQYNSTYRVVSVLTVLHQDWLNGKEYKYKVSSKALPAPIEPVISGLAKGQPERPQVYTLPGSWDELTKNQVSLTDLVKGFVQSTIAVEWESNGQPENNYGTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKTLPLSNGK
Depth of Coverage
Best scoring segments
Homo sapiens Light Chain
DNLVMTQTPKFLLVTPGEPATITLRSSQSLLNENGYNYKYWYQKKPGQSPQLLIYQASTRASGVPDRFGSPRYGTGGSDFISRVQAEDLAVPECHQDLQSPTFGAGTKLEIKTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPRLAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFGRNEC
Depth of Coverage
Best scoring segments
1403 (12.41% of all input reads) reads where matched to this segment of these 370 (26.37% of all matched reads) were matched uniquely.
618 (5.46% of all input reads) reads where matched to this segment of these 60 (9.71% of all matched reads) were matched uniquely.
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGHG3 | 377 | 3.789E+04 | 431 | 236 | 3 |
| IGHG4 | 327 | 3.111E+04 | 348 | 83 | 1 |
| IGHG2 | 326 | 3.093E+04 | 344 | 141 | 2 |
| IGHV3-9 | 119 | 1707 | 26 | 0 | 0 |
| IGHV3-43 | 119 | 1688 | 26 | 0 | 0 |
| IGHM | 453 | 1256 | 20 | 1076 | 17 |
| IGHV3-30 | 118 | 1143 | 15 | 0 | 0 |
| IGHV3-33 | 118 | 1123 | 14 | 0 | 0 |
| IGHV3-30-5 | 118 | 981 | 13 | 0 | 0 |
| IGHV3-20 | 118 | 972 | 15 | 0 | 0 |
| IGHV2-26 | 120 | 967 | 17 | 274 | 4 |
| IGHV2-70 | 120 | 905 | 15 | 211 | 3 |
| IGHA1 | 323 | 890 | 13 | 110 | 2 |
| IGHV3-NL1 | 118 | 874 | 11 | 0 | 0 |
| IGHV3-53 | 117 | 867 | 12 | 140 | 2 |
| IGHV3-74 | 118 | 829 | 11 | 0 | 0 |
| IGHA2 | 310 | 780 | 11 | 0 | 0 |
| IGHV3-7 | 118 | 757 | 11 | 0 | 0 |
| IGHV1-18 | 118 | 738 | 11 | 142 | 2 |
| IGHV3-21 | 118 | 737 | 11 | 0 | 0 |
| IGHV3-13 | 117 | 733 | 10 | 0 | 0 |
| IGHV3-66 | 117 | 727 | 10 | 0 | 0 |
| IGHV3-48 | 118 | 712 | 10 | 0 | 0 |
| IGHV3-23 | 118 | 660 | 10 | 0 | 0 |
| IGHV3-11 | 118 | 633 | 9 | 0 | 0 |
| IGHV6-1 | 121 | 598 | 10 | 49 | 1 |
| IGHV3-73 | 120 | 583 | 12 | 447 | 9 |
| IGHV3-64 | 118 | 525 | 8 | 0 | 0 |
| IGHV3-15 | 120 | 460 | 8 | 115 | 2 |
| IGHV2-5 | 120 | 437 | 9 | 46 | 1 |
| IGHV4-4 | 118 | 397 | 6 | 0 | 0 |
| IGHV3-72 | 120 | 376 | 6 | 0 | 0 |
| IGHV1-69 | 118 | 358 | 5 | 0 | 0 |
| IGHE | 428 | 348 | 7 | 137 | 3 |
| IGHV4-59 | 117 | 295 | 4 | 0 | 0 |
| IGHV4-39 | 119 | 274 | 4 | 0 | 0 |
| IGHJ1 | 37 | 259 | 4 | 0 | 0 |
| IGHV1-46 | 118 | 252 | 3 | 0 | 0 |
| IGHV1-8 | 118 | 252 | 3 | 0 | 0 |
| IGHV1-3 | 118 | 252 | 3 | 0 | 0 |
| IGHV1-45 | 118 | 252 | 3 | 0 | 0 |
| IGHV4-34 | 117 | 250 | 4 | 45 | 1 |
| IGHV4-30-4 | 119 | 225 | 3 | 0 | 0 |
| IGHV3-49 | 120 | 224 | 4 | 63 | 1 |
| IGHJ5 | 36 | 204 | 3 | 0 | 0 |
| IGHV1-2 | 118 | 189 | 3 | 105 | 2 |
| IGHV4-61 | 119 | 182 | 3 | 53 | 1 |
| IGHD | 385 | 156 | 3 | 106 | 2 |
| IGHV4-30-2 | 119 | 148 | 2 | 72 | 1 |
| IGHV5-51 | 118 | 101 | 1 | 0 | 0 |
| IGHV7-4-1 | 118 | 62 | 1 | 0 | 0 |
| IGHV4-28 | 118 | 59 | 1 | 0 | 0 |
| IGHV1-69-2 | 118 | 52 | 1 | 0 | 0 |
| IGHV4-38-2 | 118 | 49 | 1 | 0 | 0 |
| IGHV1-58 | 118 | 0 | 0 | 0 | 0 |
| IGHJ3 | 36 | 0 | 0 | 0 | 0 |
| IGHJ2 | 37 | 0 | 0 | 0 | 0 |
| IGHV1-24 | 118 | 0 | 0 | 0 | 0 |
| IGHV5-10-1 | 118 | 0 | 0 | 0 | 0 |
| IGHJ6 | 40 | 0 | 0 | 0 | 0 |
IGHV * IGHJ
...CAR
QQS...Best overlap (0, 0) with score 0 which results in the following sequence:
...CAR.QQ...
225 (1.99% of all input reads) reads where matched to this segment of these 72 (32.00% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGHV4-31 | 119 | 4433 | 61 | 0 | 0 |
| IGHV4-30-4 | 119 | 4375 | 60 | 0 | 0 |
| IGHV4-59 | 117 | 4137 | 57 | 0 | 0 |
| IGHV3-33 | 118 | 4037 | 56 | 854 | 15 |
| IGHV4-39 | 119 | 3953 | 55 | 0 | 0 |
| IGHV6-1 | 121 | 3325 | 50 | 1109 | 17 |
| IGHV4-61 | 119 | 3037 | 42 | 53 | 1 |
| IGHV4-34 | 117 | 2776 | 38 | 126 | 2 |
| IGHV4-30-2 | 119 | 2649 | 36 | 72 | 1 |
| IGHV4-38-2 | 118 | 2644 | 36 | 0 | 0 |
| IGHV4-4 | 118 | 2565 | 36 | 62 | 1 |
| IGHV4-28 | 118 | 2477 | 33 | 0 | 0 |
| IGHV3-30 | 118 | 2387 | 32 | 0 | 0 |
| IGHV3-9 | 119 | 2340 | 36 | 0 | 0 |
| IGHV3-30-5 | 118 | 2225 | 30 | 0 | 0 |
| IGHV2-26 | 120 | 2205 | 36 | 531 | 9 |
| IGHV3-43 | 119 | 1843 | 28 | 0 | 0 |
| IGHV3-53 | 117 | 1838 | 27 | 341 | 5 |
| IGHV3-20 | 118 | 1292 | 20 | 0 | 0 |
| IGHV3-49 | 120 | 1112 | 17 | 63 | 1 |
| IGHV3-7 | 118 | 1043 | 15 | 0 | 0 |
| IGHV2-70 | 120 | 987 | 16 | 211 | 3 |
| IGHV3-11 | 118 | 966 | 14 | 0 | 0 |
| IGHV3-NL1 | 118 | 937 | 12 | 0 | 0 |
| IGHV1-18 | 118 | 900 | 14 | 142 | 2 |
| IGHV3-74 | 118 | 829 | 11 | 0 | 0 |
| IGHV3-21 | 118 | 800 | 12 | 0 | 0 |
| IGHV3-66 | 117 | 790 | 11 | 0 | 0 |
| IGHV3-23 | 118 | 781 | 12 | 0 | 0 |
| IGHV3-48 | 118 | 775 | 11 | 0 | 0 |
| IGHV3-13 | 117 | 733 | 10 | 0 | 0 |
| IGHV3-15 | 120 | 685 | 11 | 115 | 2 |
| IGHV3-73 | 120 | 651 | 13 | 447 | 9 |
| IGHV1-69 | 118 | 631 | 10 | 61 | 1 |
| IGHV3-72 | 120 | 578 | 9 | 0 | 0 |
| IGHV3-64 | 118 | 525 | 8 | 0 | 0 |
| IGHV2-5 | 120 | 519 | 10 | 46 | 1 |
| IGHV1-46 | 118 | 506 | 7 | 0 | 0 |
| IGHV1-24 | 118 | 418 | 7 | 0 | 0 |
| IGHV1-8 | 118 | 414 | 6 | 0 | 0 |
| IGHV1-3 | 118 | 414 | 6 | 0 | 0 |
| IGHV5-10-1 | 118 | 407 | 6 | 0 | 0 |
| IGHV1-69-2 | 118 | 379 | 6 | 0 | 0 |
| IGHV5-51 | 118 | 356 | 5 | 0 | 0 |
| IGHV1-2 | 118 | 351 | 6 | 105 | 2 |
| IGHV1-45 | 118 | 252 | 3 | 0 | 0 |
| IGHV7-4-1 | 118 | 152 | 3 | 0 | 0 |
| IGHV1-58 | 118 | 0 | 0 | 0 | 0 |
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
42 (0.37% of all input reads) reads where matched to this segment of these 23 (54.76% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
595 (5.26% of all input reads) reads where matched to this segment of these 99 (16.64% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
All reads matching any Template within the CDR regions are listed here. These all stem from the alignments made in the TemplateMatching step.
CDR1
52 (0.46% of all input reads) distinct reads were matched on 33 (21.85% of all templates with CDRs) distinct templates, of these 19 (36.54% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
SMGF
FGS
SGL
S
.
.
.
Y
SLG
R
CDR2
72 (0.64% of all input reads) distinct reads were matched on 34 (22.52% of all templates with CDRs) distinct templates, of these 25 (34.72% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
AMRW
ALM
.
.
.
.
.
.
.
YWR
CDR3
41 (0.36% of all input reads) distinct reads were matched on 31 (20.53% of all templates with CDRs) distinct templates, of these 26 (63.41% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
KQR
SG
SG
FN
F
.
P
AL
YA
Y
W
858 (7.59% of all input reads) reads where matched to this segment of these 556 (64.80% of all matched reads) were matched uniquely.
| Identifier | Length | Order | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|---|
| REC-0-1_002 | 218 | IGKV2-28 → IGKJ2 → IGKC | 6.471E+04 | 858 | 5.102E+04 | 556 |
216 (1.91% of all input reads) reads where matched to this segment of these 44 (20.37% of all matched reads) were matched uniquely.
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGLC7 | 106 | 2504 | 32 | 239 | 5 |
| IGKV2-40 | 101 | 2136 | 31 | 67 | 1 |
| IGLC3 | 104 | 2136 | 23 | 0 | 0 |
| IGLC2 | 106 | 2133 | 23 | 0 | 0 |
| IGKV3-15 | 95 | 1974 | 31 | 80 | 1 |
| IGKV3-11 | 95 | 1935 | 32 | 0 | 0 |
| IGLC6 | 106 | 1865 | 20 | 0 | 0 |
| IGKV2D-29 | 100 | 1226 | 20 | 45 | 1 |
| IGLV8-61 | 98 | 1048 | 19 | 336 | 6 |
| IGKV3D-20 | 96 | 987 | 19 | 55 | 1 |
| IGLV1-44 | 98 | 956 | 16 | 0 | 0 |
| IGKV4-1 | 101 | 948 | 18 | 127 | 2 |
| IGKV2D-26 | 100 | 927 | 16 | 203 | 3 |
| IGLV1-47 | 98 | 910 | 15 | 0 | 0 |
| IGKV3-20 | 96 | 880 | 15 | 44 | 1 |
| IGKV3D-7 | 96 | 860 | 16 | 0 | 0 |
| IGKV3D-11 | 95 | 830 | 16 | 0 | 0 |
| IGLV2-14 | 99 | 704 | 12 | 69 | 1 |
| IGKV2-24 | 100 | 674 | 13 | 54 | 1 |
| IGLV1-40 | 99 | 601 | 10 | 0 | 0 |
| IGLV2-11 | 99 | 583 | 11 | 0 | 0 |
| IGLV2-23 | 99 | 561 | 10 | 0 | 0 |
| IGLV4-60 | 99 | 516 | 9 | 220 | 3 |
| IGLV2-18 | 99 | 510 | 10 | 0 | 0 |
| IGKV2-30 | 100 | 506 | 10 | 0 | 0 |
| IGKV2D-30 | 100 | 506 | 10 | 0 | 0 |
| IGKV1D-8 | 95 | 484 | 9 | 90 | 2 |
| IGLV1-36 | 98 | 462 | 8 | 62 | 1 |
| IGKV1-NL1 | 95 | 455 | 8 | 56 | 1 |
| IGKV1-33 | 95 | 442 | 8 | 46 | 1 |
| IGLV3-27 | 94 | 407 | 7 | 53 | 1 |
| IGKV5-2 | 95 | 403 | 7 | 167 | 3 |
| IGLV1-51 | 98 | 391 | 6 | 47 | 1 |
| IGKV1-6 | 95 | 387 | 7 | 0 | 0 |
| IGLV3-16 | 96 | 352 | 6 | 49 | 1 |
| IGKV1-12 | 95 | 329 | 6 | 0 | 0 |
| IGKV1-39 | 95 | 329 | 6 | 0 | 0 |
| IGKV1-27 | 95 | 329 | 6 | 0 | 0 |
| IGKV1-8 | 95 | 329 | 6 | 0 | 0 |
| IGKV1D-13 | 95 | 328 | 6 | 0 | 0 |
| IGLV2-8 | 99 | 318 | 6 | 0 | 0 |
| IGKV6-21 | 95 | 309 | 6 | 0 | 0 |
| IGLV7-43 | 98 | 297 | 5 | 0 | 0 |
| IGLV7-46 | 98 | 297 | 5 | 0 | 0 |
| IGLV3-25 | 96 | 294 | 5 | 0 | 0 |
| IGKV1D-43 | 95 | 284 | 5 | 0 | 0 |
| IGKV1-16 | 95 | 284 | 5 | 0 | 0 |
| IGKV1D-16 | 95 | 284 | 5 | 0 | 0 |
| IGKJ4 | 12 | 271 | 4 | 0 | 0 |
| IGLV6-57 | 98 | 238 | 5 | 0 | 0 |
| IGLV3-10 | 96 | 229 | 4 | 45 | 1 |
| IGLV5-52 | 105 | 228 | 4 | 114 | 2 |
| IGLV5-39 | 104 | 224 | 4 | 59 | 1 |
| IGKJ5 | 12 | 216 | 3 | 0 | 0 |
| IGKV1-9 | 95 | 199 | 4 | 45 | 1 |
| IGLV10-54 | 98 | 194 | 3 | 45 | 1 |
| IGLV3-21 | 96 | 173 | 3 | 0 | 0 |
| IGLV4-69 | 99 | 141 | 3 | 50 | 1 |
| IGKV1-17 | 95 | 122 | 2 | 0 | 0 |
| IGLV5-37 | 104 | 120 | 2 | 0 | 0 |
| IGLV5-45 | 104 | 120 | 2 | 0 | 0 |
| IGKV1-5 | 95 | 110 | 2 | 0 | 0 |
| IGLJ2 | 12 | 78 | 1 | 0 | 0 |
| IGLJ7 | 12 | 78 | 1 | 0 | 0 |
| IGKV1D-17 | 95 | 64 | 1 | 0 | 0 |
| IGLV3-9 | 95 | 55 | 1 | 0 | 0 |
| IGLV3-1 | 95 | 55 | 1 | 0 | 0 |
| IGLV3-22 | 94 | 55 | 1 | 0 | 0 |
| IGLV3-19 | 96 | 46 | 1 | 0 | 0 |
| IGKJ1 | 12 | 0 | 0 | 0 | 0 |
| IGKJ3 | 12 | 0 | 0 | 0 | 0 |
| IGLJ1 | 12 | 0 | 0 | 0 | 0 |
| IGLJ6 | 12 | 0 | 0 | 0 | 0 |
248 (2.19% of all input reads) reads where matched to this segment of these 42 (16.94% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGKV2-28 | 100 | 5696 | 79 | 168 | 2 |
| IGKV2-40 | 101 | 5575 | 78 | 0 | 0 |
| IGKV3-15 | 95 | 4683 | 68 | 80 | 1 |
| IGKV4-1 | 101 | 3903 | 58 | 127 | 2 |
| IGKV3D-7 | 96 | 3564 | 53 | 0 | 0 |
| IGKV3-20 | 96 | 3120 | 44 | 44 | 1 |
| IGKV3-11 | 95 | 2595 | 40 | 0 | 0 |
| IGKV2D-29 | 100 | 2348 | 36 | 45 | 1 |
| IGKV3D-11 | 95 | 1490 | 24 | 0 | 0 |
| IGKV3D-20 | 96 | 1443 | 26 | 55 | 1 |
| IGKV2D-26 | 100 | 1368 | 24 | 203 | 3 |
| IGLV8-61 | 98 | 1106 | 20 | 336 | 6 |
| IGKV2-24 | 100 | 994 | 19 | 54 | 1 |
| IGLV1-44 | 98 | 956 | 16 | 0 | 0 |
| IGLV3-1 | 95 | 923 | 12 | 0 | 0 |
| IGLV1-47 | 98 | 910 | 15 | 0 | 0 |
| IGLV2-14 | 99 | 896 | 15 | 69 | 1 |
| IGKV2-30 | 100 | 799 | 15 | 0 | 0 |
| IGLV2-11 | 99 | 775 | 14 | 0 | 0 |
| IGLV2-23 | 99 | 753 | 13 | 0 | 0 |
| IGLV1-40 | 99 | 731 | 12 | 0 | 0 |
| IGLV2-18 | 99 | 702 | 13 | 0 | 0 |
| IGKV2D-30 | 100 | 674 | 13 | 0 | 0 |
| IGKV1-33 | 95 | 569 | 10 | 46 | 1 |
| IGLV4-60 | 99 | 567 | 10 | 220 | 3 |
| IGLV3-16 | 96 | 547 | 9 | 49 | 1 |
| IGLV3-25 | 96 | 489 | 8 | 0 | 0 |
| IGKV1D-8 | 95 | 484 | 9 | 90 | 2 |
| IGKV6-21 | 95 | 474 | 9 | 0 | 0 |
| IGLV1-36 | 98 | 462 | 8 | 62 | 1 |
| IGKV1-NL1 | 95 | 455 | 8 | 56 | 1 |
| IGLV3-27 | 94 | 407 | 7 | 53 | 1 |
| IGKV5-2 | 95 | 403 | 7 | 167 | 3 |
| IGLV1-51 | 98 | 391 | 6 | 47 | 1 |
| IGKV1-6 | 95 | 387 | 7 | 0 | 0 |
| IGLV2-8 | 99 | 370 | 7 | 0 | 0 |
| IGLV7-43 | 98 | 356 | 6 | 0 | 0 |
| IGLV7-46 | 98 | 355 | 6 | 0 | 0 |
| IGKV1-8 | 95 | 329 | 6 | 0 | 0 |
| IGKV1-39 | 95 | 329 | 6 | 0 | 0 |
| IGKV1-27 | 95 | 329 | 6 | 0 | 0 |
| IGKV1-12 | 95 | 329 | 6 | 0 | 0 |
| IGKV1D-13 | 95 | 328 | 6 | 0 | 0 |
| IGLV5-52 | 105 | 285 | 5 | 114 | 2 |
| IGKV1D-43 | 95 | 284 | 5 | 0 | 0 |
| IGKV1-16 | 95 | 284 | 5 | 0 | 0 |
| IGKV1D-16 | 95 | 284 | 5 | 0 | 0 |
| IGKV1-9 | 95 | 241 | 5 | 45 | 1 |
| IGLV6-57 | 98 | 238 | 5 | 0 | 0 |
| IGLV3-10 | 96 | 229 | 4 | 45 | 1 |
| IGLV5-39 | 104 | 224 | 4 | 59 | 1 |
| IGKV1D-17 | 95 | 212 | 4 | 0 | 0 |
| IGLV10-54 | 98 | 194 | 3 | 45 | 1 |
| IGLV5-45 | 104 | 189 | 3 | 0 | 0 |
| IGLV3-21 | 96 | 173 | 3 | 0 | 0 |
| IGLV4-69 | 99 | 141 | 3 | 50 | 1 |
| IGKV1-17 | 95 | 122 | 2 | 0 | 0 |
| IGLV5-37 | 104 | 120 | 2 | 0 | 0 |
| IGKV1-5 | 95 | 110 | 2 | 0 | 0 |
| IGLV3-9 | 95 | 55 | 1 | 0 | 0 |
| IGLV3-22 | 94 | 55 | 1 | 0 | 0 |
| IGLV3-19 | 96 | 46 | 1 | 0 | 0 |
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
23 (0.20% of all input reads) reads where matched to this segment of these 16 (69.57% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
440 (3.89% of all input reads) reads where matched to this segment of these 404 (91.82% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
All reads matching any Template within the CDR regions are listed here. These all stem from the alignments made in the TemplateMatching step.
CDR1
42 (0.37% of all input reads) distinct reads were matched on 24 (12.24% of all templates with CDRs) distinct templates, of these 8 (19.05% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
NGS
GV
GST
.
.
SQN
RED
YGA
CDR2
67 (0.59% of all input reads) distinct reads were matched on 32 (16.33% of all templates with CDRs) distinct templates, of these 11 (16.42% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
SA
TS
.
.
.
.
.
.
ST
CDR3
22 (0.19% of all input reads) distinct reads were matched on 17 (8.67% of all templates with CDRs) distinct templates, of these 14 (63.64% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
QT
.
Y
.
.
S
S
PF
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
3029 (26.78% of all input reads) reads where matched to this segment of these 2909 (96.04% of all matched reads) were matched uniquely.
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
3032 (26.81% of all input reads) reads where matched to this segment of these 2911 (96.01% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
Length distribution
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/batchfiles/h9C12WT_mc.txt
-Run Info---------------
Version : 1.5
- Here the input can be defined, this will be used in the TemplateMatching and Recombine steps
Input ->
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3584.mztab
Name : EH3584
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3585.mztab
Name : EH3585
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3587.mztab
Name : EH3587
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3588.mztab
Name : EH3588
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3589.mztab
Name : EH3589
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3590.mztab
Name : EH3590
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3591.mztab
Name : EH3591
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3592.mztab
Name : EH3592
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3593.mztab
Name : EH3593
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3594.mztab
Name : EH3594
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3916.mztab
Name : EH3916
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3917.mztab
Name : EH3917
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3918.mztab
Name : EH3918
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3919.mztab
Name : EH3919
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3920.mztab
Name : EH3920
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3921.mztab
Name : EH3921
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3922.mztab
Name : EH3922
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3923.mztab
Name : EH3923
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3924.mztab
Name : EH3924
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3925.mztab
Name : EH3925
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3926.mztab
Name : EH3926
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3927.mztab
Name : EH3927
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4260.mztab
Name : EH4260
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4261.mztab
Name : EH4261
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4262.mztab
Name : EH4262
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4263.mztab
Name : EH4263
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4264.mztab
Name : EH4264
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4265.mztab
Name : EH4265
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4266.mztab
Name : EH4266
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4267.mztab
Name : EH4267
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4268.mztab
Name : EH4268
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4269.mztab
Name : EH4269
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4270.mztab
Name : EH4270
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4271.mztab
Name : EH4271
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4610.mztab
Name : EH4610
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4611.mztab
Name : EH4611
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4612.mztab
Name : EH4612
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4613.mztab
Name : EH4613
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4614.mztab
Name : EH4614
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4615.mztab
Name : EH4615
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4616.mztab
Name : EH4616
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4617.mztab
Name : EH4617
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4619.mztab
Name : EH4619
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4620.mztab
Name : EH4620
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5025.mztab
Name : EH5025
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5026.mztab
Name : EH5026
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5027.mztab
Name : EH5027
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5028.mztab
Name : EH5028
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5029.mztab
Name : EH5029
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5030.mztab
Name : EH5030
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5031.mztab
Name : EH5031
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5032.mztab
Name : EH5032
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5033.mztab
Name : EH5033
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5034.mztab
Name : EH5034
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5035.mztab
Name : EH5035
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5036.mztab
Name : EH5036
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5363.mztab
Name : EH5363
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5364.mztab
Name : EH5364
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5365.mztab
Name : EH5365
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5366.mztab
Name : EH5366
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5367.mztab
Name : EH5367
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5368.mztab
Name : EH5368
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5369.mztab
Name : EH5369
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5370.mztab
Name : EH5370
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5371.mztab
Name : EH5371
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5372.mztab
Name : EH5372
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5373.mztab
Name : EH5373
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5374.mztab
Name : EH5374
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5724.mztab
Name : EH5724
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5725.mztab
Name : EH5725
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5726.mztab
Name : EH5726
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5727.mztab
Name : EH5727
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5728.mztab
Name : EH5728
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5729.mztab
Name : EH5729
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5730.mztab
Name : EH5730
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5731.mztab
Name : EH5731
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5732.mztab
Name : EH5732
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5733.mztab
Name : EH5733
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5734.mztab
Name : EH5734
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5735.mztab
Name : EH5735
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6082.mztab
Name : EH6082
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6083.mztab
Name : EH6083
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6084.mztab
Name : EH6084
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6085.mztab
Name : EH6085
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6086.mztab
Name : EH6086
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6087.mztab
Name : EH6087
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6088.mztab
Name : EH6088
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6089.mztab
Name : EH6089
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6090.mztab
Name : EH6090
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6091.mztab
Name : EH6091
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6092.mztab
Name : EH6092
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6093.mztab
Name : EH6093
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6613.mztab
Name : EH6613
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6614.mztab
Name : EH6614
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6615.mztab
Name : EH6615
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6616.mztab
Name : EH6616
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6617.mztab
Name : EH6617
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6618.mztab
Name : EH6618
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6619.mztab
Name : EH6619
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6620.mztab
Name : EH6620
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6621.mztab
Name : EH6621
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6622.mztab
Name : EH6622
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6623.mztab
Name : EH6623
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6624.mztab
Name : EH6624
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8103.mztab
Name : EH8103
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8104.mztab
Name : EH8104
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8105.mztab
Name : EH8105
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8106.mztab
Name : EH8106
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8107.mztab
Name : EH8107
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8108.mztab
Name : EH8108
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8109.mztab
Name : EH8109
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8110.mztab
Name : EH8110
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8111.mztab
Name : EH8111
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8112.mztab
Name : EH8112
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8113.mztab
Name : EH8113
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8114.mztab
Name : EH8114
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7333.mztab
Name : EH7333
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7334.mztab
Name : EH7334
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7335.mztab
Name : EH7335
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7336.mztab
Name : EH7336
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7337.mztab
Name : EH7337
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7338.mztab
Name : EH7338
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7339.mztab
Name : EH7339
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7340.mztab
Name : EH7340
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7341.mztab
Name : EH7341
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7342.mztab
Name : EH7342
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7343.mztab
Name : EH7343
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7344.mztab
Name : EH7344
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7678.mztab
Name : EH7678
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7679.mztab
Name : EH7679
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7680.mztab
Name : EH7680
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7681.mztab
Name : EH7681
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7682.mztab
Name : EH7682
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7683.mztab
Name : EH7683
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7684.mztab
Name : EH7684
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7685.mztab
Name : EH7685
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7686.mztab
Name : EH7686
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7687.mztab
Name : EH7687
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7688.mztab
Name : EH7688
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7689.mztab
Name : EH7689
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8446.mztab
Name : EH8446
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8447.mztab
Name : EH8447
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8448.mztab
Name : EH8448
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8449.mztab
Name : EH8449
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8450.mztab
Name : EH8450
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8451.mztab
Name : EH8451
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8452.mztab
Name : EH8452
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8453.mztab
Name : EH8453
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8454.mztab
Name : EH8454
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8455.mztab
Name : EH8455
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8456.mztab
Name : EH8456
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8457.mztab
Name : EH8457
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9283.mztab
Name : EH9283
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9284.mztab
Name : EH9284
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9285.mztab
Name : EH9285
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9286.mztab
Name : EH9286
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9287.mztab
Name : EH9287
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9288.mztab
Name : EH9288
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9289.mztab
Name : EH9289
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9290.mztab
Name : EH9290
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9291.mztab
Name : EH9291
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9292.mztab
Name : EH9292
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9293.mztab
Name : EH9293
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9294.mztab
Name : EH9294
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9661.mztab
Name : EH9661
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9662.mztab
Name : EH9662
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9663.mztab
Name : EH9663
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9664.mztab
Name : EH9664
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9665.mztab
Name : EH9665
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9666.mztab
Name : EH9666
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9667.mztab
Name : EH9667
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9668.mztab
Name : EH9668
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9669.mztab
Name : EH9669
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9670.mztab
Name : EH9670
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9671.mztab
Name : EH9671
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9672.mztab
Name : EH9672
CutoffScore: 0.8
-FilterPPM : 100
<-
<-
- Template matching matches the reads defined in 'Input' to the given Templates defined in the different groups in the 'Segments'
TemplateMatching ->
EnforceUnique : 0.9
CutoffScore : 15
AmbiguityThreshold : 0.9
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/alphabets/mass_alphabet.txt)
Segments->
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Heavy_Chain.txt)
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Light_Chain.txt)
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/common_contaminants.txt)
<-
<-
Recombine->
-Pick the highest scoring templates from each segment
N : 1
Decoy : True
CutoffScore : 10
-Separated by whitespace means directly attached
-Separated by * means with a gap attached
Order->
Homo sapiens Heavy Chain: IGHV * IGHJ IGHC
Homo sapiens Light Chain: IGLV IGLJ IGLC
<-
<-
Report ->
Folder: /storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/results/{datetime} {name}/
HTML ->
Path: report-monoclonal_h9C12WT.html
<-
FASTA ->
Path: report-monoclonal-tm_h9C12WT.fasta
OutputType: TemplateMatching
<-
CSV ->
Path: report-monoclonal-tm_h9C12WT.csv
OutputType: TemplateMatching
<-
FASTA ->
Path: report-monoclonal-rec_h9C12WT.fasta
OutputType: Recombine
<-
CSV ->
Path: report-monoclonal-rec_h9C12WT.csv
OutputType: Recombine
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/alphabets/mass_alphabet.txt
Alphabet ->
Characters : ARNDCQEGHILKMFPSTWYVBZXJ.*
Identity : 8
Mismatch : -1
GapStart : -12
GapExtend : -1
PatchLength: 3
Swap : 2
Symmetric sets ->
Score: 8
Sets :>
I,L,J
<:
<-
Symmetric sets ->
Score: 6
Sets :>
N,GG
Q,AG
AV,GL,GI,GJ
AN,QG,AGG
LS,IS,JS,TV
AM,CV
NV,AAA,GGV
NT,QS,AGS,GGT
LN,IN,JN,QV,AGV,GGL,GGI,GGJ
DL,DI,DJ,EV
QT,AAS,AGT
AY,FS
LQ,IQ,AAV,AGL,AGI,AGJ
NQ,ANG,QGG
KN,GGK
EN,DQ,ADG,EGG
DK,AAT,GSV
MN,AAC,GGM
AS,GT
AAL,AAI,AAJ,GVV
QQ,AAN,AQG
EQ,AAD,AEG
EK,ASV,GLS,GIS,GJS,GTV
MQ,AGM,CGV
AAQ,NGV
<:
<-
Asymmetric sets ->
Score: 1
Sets :>
X->A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z -Remove mismatch penalty on single gaps
A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z->X -Remove mismatch penalty on single gaps
<:
<-
Asymmetric sets ->
Score: -4
Sets :>
.->A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z -Add additional penalty on bigger gaps
A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z->. -Add additional penalty on bigger gaps
<:
<-
Asymmetric sets ->
Score: 3
Sets :>
- Template sequence -- results -> in read sequence - Type
Q->E -Deamidation
N,GG->D -Deamidation
T->D -Methylation
S->T -Methylation
D->E -Methylation
R->AV,GL,GI,GJ -Methylation
Q->AA -Methylation
W->DS,AM,CV,TT -Oxidation
M->F -Oxidation
S->E -Acetylation
K->AV,GL,GI,GJ -Acetylation/Homoarginine
<:
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Heavy_Chain.txt
Homo sapiens Heavy Chain->
Segment->
Path : Homo_sapiens_IGHV.fasta
Name : IGHV
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGHJ.fasta
Name : IGHJ
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGHC.fasta
Name : IGHC
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Light_Chain.txt
Homo sapiens Light Chain->
Segment->
Path : Homo_sapiens_IGKV,IGLV.fasta
Name : IGLV
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGKJ,IGLJ.fasta
Name : IGLJ
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGKC,IGLC.fasta
Name : IGLC
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/common_contaminants.txt
Decoy ->
Segment ->
Path: common_contaminants.fasta
Name: Decoy
Identifier: ^sp\|[\w]*\|([\w]+)_
<-
<-
Answers to common questions can be found here. If anything is unclear, or you miss any features please reach out to the authors, all information can be found on the repository.
If the graphs are needed in a vector graphics format the whole page can be printed to a pdf. To do this print the page to a pdf file and save the generated file. These files can be imported in most vector graphics editors. It is best to turn on the background graphics and turn off any headers, besides this setting the margins smaller and using landscape or portrait could enhance the results. See the below picture for the options. If you want to be able to edit the text as text in Adobe Illustrator we had the best results using Firefox > Print > Save as PDF.
Or click here to print
The Roepstorff, Fohlman, Johnson ion nomenclature is used. This is the common way of naming ions most people will be familiar with. But we use two special ions, w and d also called satellite ions, which are not commonly used. These form by cleavages of the side chain and are thus specially suited for the disambiguation of Leucine and Isoleucine. In the overview below the mass differences and ions formed are displayed. The d ion is formed by fragmentation of the side chain of an a ion. The w ion is formed by side chain fragmentation of a z ion. Because isoleucine and threonine are doubly substituted at the beta carbon these two amino acids form two different w/d ions. THese ions are not formed with all fragmentation techniques though, Stitch only searches for d ions in the first amino acids with CID/HCD/PQD data, and only searches for w ions in ETD/ECD/EThcD/ETciD data.
Find more information here.